GSM7383699: NoiseControl_Sample15_Bulk-Population-15; Cricetulus griseus; RNA-Seq
80,000 to 120,000 cells were collected for extraction and for fed-batch flasks, 1 to 5 million cells were used for extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen, Germantown, MD) following manufacturer's protocol. All RNA samples were run on the Agilent5200 Fragment Analyzer (Agilent, Santa Clara, CA) to verify RNA quality prior to submission for sequencing. Samples with an RNA integrity number of  6.0 or greater and at least 100 ng of high quality RNA were sent for sequencing, as quantified by measuring absorbance at 260 and 280 nm using the DS-11 nanospectrophotometer (DeNovix, Wilmington, DE). Samples were stored at -80°C prior to shipment RNA library preparation, sequencing and analysis was conducted at Azenta Life Sciences (South  Plainfield, NJ, USA) as follows:  The RNA samples received were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific,  Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto,  CA, USA).  The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina  using manufacturer's instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially  enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand  and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and  adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition  and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent  TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer  (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems,  Wilmington, MA, USA).  The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was  loaded onto the Illumina HiSeq instrument according to manufacturer's instructions. The samples were  sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were  conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina    HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-  match was allowed for index sequence identification.